bims-tricox 2024-05-05 papers

Issue of 2024–05–05
two papers selected by
Yash Verma, University of Zurich

Biochem Soc Trans. 2024 May 02. pii: BST20231106. [Epub ahead of print]

Ribosomal RNA expansion segments and their role in ribosome biology.

Ribosomes are universally conserved cellular machines that catalyze protein biosynthesis. The active sites underly immense evolutionary conservation resulting in virtually identical core structures of ribosomes in all domains of life including organellar ribosomes. However, more peripheral structures of cytosolic ribosomes changed during evolution accommodating new functions and regulatory options. The expansion occurred at the riboprotein level, including more and larger ribosomal proteins and at the RNA level increasing the length of ribosomal RNA. Expansions within the ribosomal RNA occur as clusters at conserved sites that face toward the periphery of the cytosolic ribosome. Recent biochemical and structural work has shed light on how rRNA-specific expansion segments (ESs) recruit factors during translation and how they modulate translation dynamics in the cytosol. Here we focus on recent work on yeast, human and trypanosomal cytosolic ribosomes that explores the role of two specific rRNA ESs within the small and large subunit respectively. While no single regulatory strategy exists, the absence of ESs has consequences for proteomic stability and cellular fitness, rendering them fascinating evolutionary tools for tailored protein biosynthesis.

Keywords: cotranslational factor recruitment; nascent peptide chain maturation; rRNA expansion segments; translation elongation; translation regulation

DOI: https://doi.org/10.1042/BST20231106

Front Mol Biosci. 2024 ;11 1395220

Implication of Stm1 in the protection of eIF5A, eEF2 and tRNA through dormant ribosomes.

Mengtan Du, Xin Li, Wanlin Dong, Fuxing Zeng.

Background: Dormant ribosomes are typically associated with preservation factors to protect themselves from degradation under stress conditions. Stm1/SERBP1 is one such protein that anchors the 40S and 60S subunits together. Several proteins and tRNAs bind to this complex as well, yet the molecular mechanisms remain unclear. Methods: Here, we reported the cryo-EM structures of five newly identified Stm1/SERBP1-bound ribosomes. Results: These structures highlighted that eIF5A, eEF2, and tRNA might bind to dormant ribosomes under stress to avoid their own degradation, thus facilitating protein synthesis upon the restoration of growth conditions. In addition, Ribo-seq data analysis reflected the upregulation of nutrient, metabolism, and external-stimulus-related pathways in the ∆stm1 strain, suggesting possible regulatory roles of Stm1. Discussion: The knowledge generated from the present work will facilitate in better understanding the molecular mechanism of dormant ribosomes.

Keywords: SERBP1; cryo-EM; dormant ribosome; eEF2; stm1

DOI: https://doi.org/10.3389/fmolb.2024.1395220